showLogo: Show RcisTarget as HTML

In aertslab/RcisTarget: RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Show RcisTarget as HTML

Description

Shows the results motif enrichment table as an HTML including the motif logos. Note that Transfac-Pro logos cannot be shown.

Usage

showLogo(
  motifEnrDT,
  motifCol = c("motif", "bestMotif", "MotifID"),
  dbVersion = NULL,
  nSignif = 3,
  colsToShow = c(motifEnrichment = c("motifDb", "logo", "NES", "geneSet", "TF_highConf"),
    regulonTargets = c("TF", "gene", "nMotifs", "bestMotif", "logo", "NES",
    "highConfAnnot", "Genie3Weight")),
  options = list(pageLength = 50),
  ...
)

Arguments

motifEnrDT	Results from RcisTarget (data.table)
motifCol	Name of the column which contains the logo ID.
dbVersion	For current databases (version 10) use "v10nr_clust"
nSignif	Number of digits to show in numeric columns.
colsToShow	Columns to show in the HTML (by default, the list of the enriched genes is hidden)
options	List of options to pass to DT::databable
...	Other arguments to pass to DT::databable

Value

Returns the DT::datatable() object which can be shown as HTML.

See Also

See the package vignette for more examples: vignette("RcisTarget")

Examples

# Run the enrichment (or load previous results)
load(paste(file.path(system.file('examples', package='RcisTarget')),
           "motifEnrichmentTable_wGenes.RData", sep="/"))

# Show table as HTML
showLogo(motifEnrichmentTable_wGenes)

aertslab/RcisTarget documentation built on March 7, 2024, 11:21 p.m.